In Fallout 2, the Enclave are the remnants of the US government. They believe themselves to be the legitimate rulers of the world, and view all other humans except for those still in vaults to be genetically contaminated subhuman mutants. Throughout the game they capture and experiment on people to perfect a modified version of FEV (the virus that creates supermutants and other types of mutants) that will be released into the atmosphere and kill off all humans (except for the Enclave, who will inoculate themselves).
In Fallout 3, the Enclave are still around even after they got nuked and their leaders killed because there was a computer president backed up somewhere. Now they have another strain of FEV, only this one will only work if it's poured into a basin (a part of the Potomac), and the only way for people to drink from this one specific basin is to purify it with your dad's water purifier, which, there's a LOT of problems with this plan but okay. Anyway, this "kill everyone in this very specific locale for reasons" plan is only really by backed by Computer Prez, while Colonel Autumn thinks that's dumb and that if they just turn on the water (which everyone wants to turn on) then people will want to be the Enclave's subjects out of gratitude for giving them drinking water, which sounds perfectly reasonable so you have to fight them.